Introduction

Data Source

Sample Data

Below are the metadata associated with each sample, as provided by LifeMine.

S000565

Feature Counts

The table below contains the normalized feature counts per locus ID for each sample.

S000565

Genes in Cluster

This is the clustergenes table as provided by LifeMine, which contains the genes and locus IDs from the cluster of interest.

S000565

Quality Control

Violin Plots

Let’s take a quick look at the distribution of counts for each sample.

Expressed genes

The following is a table of the number of expressed genes in each samples, giving a quantititive value to the quality of the expression data. Two thresholds for normalized gene expression were used here: 0.5 and 1.

S000565

ERCC controls

Shown here are some simple plots of ERCC concentrations after normalization.

S000565_WT_NA_1 vs. S000565_WT_NA_2

S000565_WT_NA_1 vs. S000565_S000631_PKS_KO_NA_1

S000565_WT_NA_1 vs. S000565_S000631_PKS_KO_NA_2

S000565_WT_NA_1 vs. S000565_TF_KI_NA_1

S000565_WT_NA_1 vs. S000565_TF_KI_NA_2

S000565_WT_NA_1 vs. S000565_S000631_TF_KI_NA_2

S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_NA_1

S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_NA_2

S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_NA_3

S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_NA_4

S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_NA_6

S000565_WT_NA_1 vs. S000565_WT_NA_1

S000565_WT_NA_1 vs. S000565_WT_NA_2

S000565_WT_NA_1 vs. S000565_S000631_PKS_KO_NA_1

S000565_WT_NA_1 vs. S000565_S000631_PKS_KO_NA_2

S000565_WT_NA_1 vs. S000565_TF_KI_NA_1

S000565_WT_NA_1 vs. S000565_TF_KI_NA_2

S000565_WT_NA_1 vs. S000565_S000631_TF_KI_NA_1

S000565_WT_NA_1 vs. S000565_S000631_TF_KI_NA_2

S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_NA_1

S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_NA_2

S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_NA_3

S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_NA_4

S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_NA_5

S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_NA_6

S000565_WT_NA_1 vs. S000565_WT_NA_1

S000565_WT_NA_1 vs. S000565_WT_NA_2

S000565_WT_NA_1 vs. S000565_S000631_PKS_KO_no41_NA_1

S000565_WT_NA_1 vs. S000565_S000631_PKS_KO_no41_NA_2

S000565_WT_NA_1 vs. S000565_TF_KI_no10_NA_1

S000565_WT_NA_1 vs. S000565_TF_KI_no10_NA_2

S000565_WT_NA_1 vs. S000565_S000631_TF_KI_no1_NA_1

S000565_WT_NA_1 vs. S000565_S000631_TF_KI_no1_NA_2

S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_no3_NA_1

S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_no3_NA_2

S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_no13_NA_1

S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_no13_NA_2

S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_no15_NA_1

S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_no15_NA_2

Differential expression

Volcano plot

This volcano plot shows us a summary view of the differential expression results. Each point on the plot represents one gene in the experiment. Mouse over a point to see a pop-up view with details on the results for that gene. Interactive plots like this are computationally intensive, so we’re only showing here the genes that have a p-value of p <= 0.05.

The y-axis position represents the -log p-value: a higher value indicates that the gene is more significant. The x-axis position shows the log-fold-change for the gene between the engineered and wild-type samples. Genes on the right-hand side of the plot increase in expression in the engineered sample. Genes on the left-hand side decrease in expression in the engineered sample.

Treatment1-Day4 vs. Control-Day4

Treatment2-Day4 vs. Control-Day4

Treatment2-Day4 vs. Control-Day4

Treatment2-Day4 vs. Control-Day4

Treatment1-Day7 vs. Control-Day7

Treatment2-Day7 vs. Control-Day7

Treatment3-Day7 vs. Control-Day7

Treatment4-Day7 vs. Control-Day7

Treatment1-Day14 vs. Control-Day14

Treatment2-Day14 vs. Control-Day14

Treatment3-Day14 vs. Control-Day14

Treatment4-Day14 vs. Control-Day14

Full table

The full list of differentially expressed genes can be found in the tables below. Click the “Download” button to view a version of the data in Excel.

  description
symbol The locus ID of the gene.
statistic The test statistic for this gene. This statistic is an intermediate value used to calculate the p-value.
baseMean The mean expression value across all samples in the analysis.
log2FC The log2-fold-change of gene expression between the engineered strain and wild-type control
padj The p-value for this gene, corrected for multiple testing.

Treatment1-Day4 vs. Control-Day4

There are 1 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.

Treatment2-Day4 vs. Control-Day4

There are 9 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.

Treatment2-Day4 vs. Control-Day4

There are 9 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.

Treatment2-Day4 vs. Control-Day4

There are 9 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.

Treatment1-Day7 vs. Control-Day7

There are 0 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.

Treatment2-Day7 vs. Control-Day7

There are 12 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.

Treatment3-Day7 vs. Control-Day7

There are 8 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.

Treatment4-Day7 vs. Control-Day7

There are 128 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.

Treatment1-Day14 vs. Control-Day14

There are 0 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.

Treatment2-Day14 vs. Control-Day14

There are 0 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.

Treatment3-Day14 vs. Control-Day14

There are 7 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.

Treatment4-Day14 vs. Control-Day14

There are 11 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.

Barplots

Below are barplots of the normalized read counts for each locus ID within a CDK cluster.

ORF1_MeT_LM541

GN003446.00_002768

ORF2_ETaG_LM565

GN003446.00_003104

ORF3_Unk_LM541

GN003446.00_002654

ORF4_VOC_LM565

GN003446.00_002608

ORF5_SDR_LM565

GN003446.00_002540

ORF6_hydrolase_LM565

GN003446.00_002439

ORF7_P450_LM565

GN003446.00_002333

ORF8_P450_LM565

GN003446.00_002184

ORF9_PKS_LM565

GN003446.00_001767

ORF9_PKS_LM565-KO

GN003446.00_001767-KO

ORF10_transport_LM565

GN003446.00_002892

ORF11_TF_LM565

GN003446.00_001668

all

Conclusions

R session info

This section includes technical details about the R code used to produce this analysis. Most readers can safely ignore it.

##  setting  value                       
##  version  R version 3.6.0 (2019-04-26)
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##  system   x86_64, darwin17.7.0        
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##  language (EN)                        
##  collate  en_US.UTF-8                 
##  ctype    en_US.UTF-8                 
##  tz       America/New_York            
##  date     2020-07-06
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